Biological molecular motors provide most cells with the dynamic systems required for their day-to-day existence. Examples occur in even the simplest organism (e.g. a bacteria virus), and the range of tasks that they carry out is vast. Over the last few years, there has been a large increase in the study of these motors, and it is becoming apparent that many motors will find uses in either bionanotechnology or synthetic biology.
Molecular Motors in Bionanotechnology describes a wide range of molecular motors, ranging from chemical motors to biological motors, in a manner that updates, or reviews, both classification of the type of motor and the grouping into families. Many techniques have evolved to study and characterise molecular motors at the single-molecule level (e.g. use of molecular tweezer devices for single-molecule studies). The text introduces the reader to the concepts and benefits of these techniques. In addition, it looks at the structural information and how this helps understand function and, finally, how some of these motors are being used or may be used in the future as part of a synthetic biology approach to building devices and sensors.
Preface
Acknowledgement
1 Mode of Activity of Molecular Motors
1.1 Power-Stroke Model of Motion
1.2 Brownian Ratchet Model of Motion
1.3 Motor Efficiency
2 Chemical Motors
2.1 Rotary Chemical Motors
2.1.1 Helicene-Based Motors
2.1.2 A Chemical Motor Incorporating a Chiral Carbon-Carbon Double Bond
2.1.3Rotaxane-Based Rotary Motors
2.2 Linear Chemical Motors
2.2.1 Rotaxane-Based Linear Motors
2.2.2 DNA-Based Molecular Motors
2.3 Potential for Use of Chemical Motors in Bio nanotechnology
3 Biological Motors that Produce Rotary Motion
3.1 ATP Synthase
3.1.1 Subunit Nomenclature
3.1.2Mechanism of Motor Action
3.1.3 Single-Molecule Analysis of Motor Activity
3.1.4 Structural Details of the Motor
3.2 Bacterial Flagella Motor
3.2.1 Direction Switching of Flagella Motor
3.2.2 Structural Outline of Flagella Motor
2.2.3 Subunit Nomenclature
3.2.4 Mechanism of Motor Activity
3.3 P-Type Ion Pumps
3.4 Bacteriophage DNA-Loading Motors
3.4.1 Structural Features of DNA-Packaging Motors
3.5 Potential for Using Biological Rotary Motors in Bio nanotechnology
4 Biological Motors that Produce Linear Motion
4.1 Kinesins
4.1.1 Nomenclature
4.1.2 General Features of the Kinesin Superfamily Proteins (KIFs)
4.1.3 Kinesin Families
4.1.3.1 Kinesin-1 family
4.1.3.2 Kinesin-2 family
4.1.3.3 Kinesin-3 family
4.1.3.4 Kinesin-4 family
4.1.3.5 Kinesin-5 family
4.1.3.6 Kinesin-6 family
4.1.3.7 Kinesin-7 family
4.1.3.8 Kinesin-8 family
4.1.3.9 Kinesin-9 family
4.1.3.10 Kinesin-10 family
4.1.3.11 Kinesin-11 family
4.1.3.12 Kinesin-12 family
4.1.3.13 Kinesin-13 family
4.1.3.14 Kinesin-14 family
4.1.3.15 Orphans
4.1.4 Structure and Mechanism
4.2 Myosin Superfamily
4.2.1 Function
4.2.2 Myosin Complex
4.2.3 Nomenclature
4.2.4 Classification
4.2.4.1 Myosin-I
4.2.4.2 Myosin-II or "conventional" myosins
4.2.4.3 Myosin-III
4.2.4.4 Myosin-IV
4.2.4.5 Myosin-V
4.2.4.6 Myosin-VI
4.2.4.7 Myosin-VII
4.2.4.8 Myosin-VIII
4.3.4.8 Myosin-VIIII
4.2.4.9 Myosin-IX
4.2.4.10 Myosin-X
4.2.4.11 Myosin XI
4.2.4.12 Myosin XII
4.2.4.13 Myosin XIII
4.2.4.14 Myosin XIV
4.2.4.15 Myosin XV
4.2.4.16 Myosin XVI
4.2.4.17 Myosin XVII
4.2.4.18 Myosin XVIII
4.2.4.19 Myosin XIX
4.2.4.20 Myosin XX
4.2.4.21 Myosin XXI
4.2.4.22 Myosin XXII
4.2.4.23 Myosin XXIII
4.2.4.24 Myosin XXIV
4.2.5 Structure and Mechanism
4.3 Dyneins
4.3.1 Function
4.3.2 Dynein Complexes
4.3.3 Nomenclature
4.3.4 Classification
4.3.5 Axonemal Dyneins
4.3.5.1 Function
4.3.6 Families
4.3.7 Structure and Mechanism
4.3.8 Cytoplasmic Dyneins
4.3.8.1 Function
4.3.9 Families
4.3.10 Structure
4.3.11 Mechanism
4.4 Helicases and Translocases
4.4.1 Function
4.4.2 Classification
4.4.3 Superfamily I (SF1)
4.4.3.1 SF1A helicases
4.4.3.2 SF1B helicases
4.4.4 Superfamily 2 (SF2)
4.4.4.1 SF2a subfamilies
4.4.4.2 SF2B subfamily
4.4.5 Chromatin Remodeling Complexes
4.4.6 Superfamilies 3-6
4.4.6.1 Superfamily 3
4.4.6.2 Superfamily 4
4.4.6.3 Superfamily 5
4.4.6.4 Superfamily 6
4.4.7 Other Hexameric Translocases
4.4.7.1 F1-ATPase-like (three-site sequential) model
4.4.7.2 All sites sequential model
4.4.7.3 Stochastic model
4.4.7.4 Concerted model
4.4.8 Structural Homology Between Helicase and Translocase ATPase Domains
4.4.9 A conserved ATPase Site Mechanism
4.4.10 Characterization of Helicases/Translocases
4.4.10.1 Rate of translocation
4.4.10.1 Rate of translocation
4.4.10.2 Direction of translocation
4.4.10.3 Processivity
4.4.10.4 Translocation step size
4.4.10.5 Active and passive enzymes
4.4.11 Potential for Use of Biological Molecular
Motorsin Bio nanotechnology
5 Towards Bio nanotechnology
5.1 Chemical Motors in Bionanotechnology
5.2 Biological Motors in Bionanotechnology
5.3 Bionanotehnology Devices in vivo
5.4 Conclusion
Bibliography
Index
Biography
James Youell has been working as a research fellow since 2004 at the University of Portsmouth on the design of a high-throughput single-molecule drug development tool utilising molecular motors. Through the development of this system, he has worked alongside a pan European research team, incorporating cutting-edge experimental tools, to build the various biological and synthetic components required. Dr Youell has published a number of papers on the development of such synthetic biology devices and given invited seminars on the subject.
Keith Firman is now retired from the University of Portsmouth, where he was reader in Molecular Biotechnology. He investigated the properties of type I restriction-modification systems. This led to the coordination of three consecutive European grants worth, in total, in excess of €4,500,000 to develop an electronic device for biosensing using single-molecule molecular motors. Dr Firman has published more than 50 papers and was also invited to participate in a number of international road-mapping exercises in nanotechnology.
